Genome Sequencing of the Japanese Eel (Anguilla japonica) for Comparative Genomic Studies on tbx4 and a tbx4 Gene Cluster in Teleost Fishes

Abstract

Limbs originated from paired fish fins are an important innovation in Gnathostomata. Many studies have focused on limb development-related genes, of which the T-box transcription factor 4 gene (tbx4) has been considered as one of the most essential factors in the regulation of the hindlimb development. We previously confirmed pelvic fin loss in tbx4-knockout zebrafish. Here, we report a high-quality genome assembly of the Japanese eel (Anguilla japonica), which is an economically important fish without pelvic fins. The assembled genome is 1.13 Gb in size, with a scaffold N50 of 1.03 Mb. In addition, we collected 24 tbx4 sequences from 22 teleost fishes to explore the correlation between tbx4 and pelvic fin evolution. However, we observed complete exon structures of tbx4 in several pelvic-fin-loss species such as Ocean sunfish (Mola mola) and ricefield eel (Monopterus albus). More interestingly, an inversion of a special tbx4 gene cluster (brip1-tbx4-tbx2b- bcas3) occurred twice independently, which coincides with the presence of fin spines. A nonsynonymous mutation (M82L) was identified in the nuclear localization sequence (NLS) of the Japanese eel tbx4. We also examined variation and loss of hindlimb enhancer B (HLEB), which may account for pelvic fin loss in Tetraodontidae and Diodontidae. In summary, we generated a genome assembly of the Japanese eel, which provides a valuable genomic resource to study the evolution of fish tbx4 and helps elucidate the mechanism of pelvic fin loss in teleost fishes. Our comparative genomic studies, revealed for the first time a potential correlation between the tbx4 gene cluster and the evolutionary development of toxic fin spines. Because fin spines in teleosts are usually venoms, this tbx4 gene cluster may facilitate the genetic engineering of toxin-related marine drugs.

Screening and identification of miRNAs regulating Tbx4/5 genes of Pampus argenteus

“…Tbx4 stimulates the formation of appendage buds and induces the formation of leg-like structures, while Tbx5 promotes the formation of wing-like appendages, indicating that Tbx4 / 5 might play key roles in limb induction ( Naiche & Papaioannou, 2003 ; Takeuchi et al, 2003 ; Naiche & Papaioannou, 2007 ). Similar mechanisms have been reported in other species, including Notophthalmus viridescens and Anguilla japonica , in which Tbx4 and Tbx5 were reported to be involved in the formation of hind limbs and forelimbs, respectively ( Simon et al, 1997 ; Khan, Linkhart & Simon, 2002 ; Chen et al, 2019 ). Silver pomfret ( Pampus argenteus ) is an economically important fish species, and its nutritive value and medicinal applications are widely known ( Xu et al, 2012 ; Zhang et al, 2014 ).…”

Tbx4 and Tbx5 gene expression associated with appendage development and its relationship with the absence of a ventral fin in Pampus argenteus

“…It can be speculated that Tbx4 is different in different species as certain genes are known to have changed, leading to their evolution and loss of certain functions; However, Tbx4-speci c DNAbinding sites and structures are highly homologous across species, suggesting the importance of Tbx4 function. Interestingly, the complete exon structure of Tbx4 was also found in in several pelvic-n-loss species such as Mola mola and Monopterus albus [32].…”

A Chromosome-level Assembly of the Japanese Eel Genome, Insights into Gene Duplication and Chromosomal Reorganization

“…This chromosome rearrangement resulted in the same haploid chromosome number (n = 25) in tarpons. Comparatively, the 19 AETK's chromosomes (Chr1, 2, 4, 7, 9-14, 16-21, 23-25) underwent 24-fusion and 18-fission to form the 13 chromosomes (Chr1- 8,11,13,[15][16][17] in Japanese eels (Supplementary Table 14). The…”

“…A draft genome of the American eel (with a total size of 1.41 GB) was published in 2017, and 26,564 genes were annotated 73 . In 2019, the assembly of a Japanese genome of 1.13 Gb 17 was improved with 256,649 contigs, 41,687 scaffolds, and a scaffold N50 of 1.03M. Currently, only the draft genome is available for Japanese eels.…”